Results

To elucidate the consequences of the common JNCL mutation in neuronal cells, we used P4 knock-in mouse cerebella to establish conditionally immortalized CbCln3 wild-type, heterozygous, and homozygous neuronal precursor cell lines, which can be differentiated into MAP-2 and NeuN-positive, neuron-like cells. Homozygous CbCln3Δex7/8 precursor cells express low levels of mutant battenin and, when aged at confluency, accumulate ATPase subunit c. Recessive phenotypes are also observed at sub-confluent growth; cathepsin D transport and processing are altered, although enzyme activity is not significantly affected, lysosomal size and distribution are altered, and endocytosis is reduced. In addition, mitochondria are abnormally elongated, cellular ATP levels are decreased, and survival following oxidative stress is reduced.

Conclusions

These findings reveal that battenin is required for intracellular membrane trafficking and mitochondrial function. Moreover, these deficiencies are likely to be early events in the JNCL disease process and may particularly impact neuronal survival.

The pathological hallmark of JNCL is autofluorescent ceroid lipofuscin deposits within autolysosomes that are enriched in subunit c of the mitochondrial ATP synthase complex [3–5]. Remarkably, these deposits are not only found in CNS neurons but are also abundant in non-neuronal cells outside of the nervous system. The relationship of subunit c deposits to the JNCL disease process, and the underlying reason for the neuronal specificity of the disease remain poorly understood.

The CLN3-encoded protein (battenin, also called CLN3 or cln3 p) is a highly conserved, ubiquitously expressed, multi-pass membrane protein [6] that localizes to the lysosome and other vesicular compartments [7–9]. Battenin function remains to be elucidated, although studies of btn1, the yeast CLN3 ortholog, have implicated battenin in lysosomal pH homeostasis and amino acid transport [10, 11].

To explore JNCL pathogenesis and battenin function, we previously generated a genetically precise JNCL mouse model. Cln3Δex7/8 knock-in mice harbor the ~1 kb common JNCL mutation and express a non-truncated mutant battenin isoform that is detectable with antibodies recognizing C-terminal epitopes. Homozygous Cln3Δex7/8 knock-in mice exhibit a progressive JNCL-like disease, with perinatal onset of subunit c deposition in many cell types and later onset of neuronal dysfunction and behavioral deficits [12]. These findings suggest that the major JNCL defect leads to abnormal turnover of mitochondrial subunit c, in a manner that selectively compromises CNS neurons.

Currently, there is no suitable neuronal cell system to investigate the impact of the common JNCL mutation on biological processes. Therefore, we have established cerebellar neuronal precursor cell lines from Cln3Δex7/8 knock-in mice. Homozygous CbCln3Δex7/8 cells exhibit pathological hallmarks of the disease, and a survey of membrane organelles revealed membrane trafficking defects and mitochondrial dysfunction in homozygous mutant CbCln3Δex7/8 cells.

Results

Generation of a genetically precise cerebellar JNCL cell model

To generate a precise genetic, neuron-derived JNCL cell culture system, we immortalized granule neurons cultured from postnatal day 4 (P4) cerebella of homozygous and heterozygous Cln3Δex7/8 knock-in mice, and wild-type littermates. Primary cell cultures enriched for granule neurons were transduced with retroviral vector bearing a selection cassette and temperature-sensitive tsA58 SV40 large T antigen. Growth in G418 containing medium at the permissive temperature (33°C) allowed for selection and isolation of multiple clonal nestin-positive (Fig. 1a), and GFAP-negative (Fig. 1b), cell lines for each genotype. No genotype specific differences were observed in cellular morphology or doubling time (~46 hours) (data not shown). As expected, SV40 large T antigen expression was rapidly lost and cell division ceased when cells were shifted to the non-permissive temperature (39°C) (data not shown). Upon addition of neuronal differentiation cocktail, precursor cells became neuron-like in morphology and exhibited decreased nestin expression (data not shown) and increased MAP2 and NeuN expression (Fig. 1c,1d), but not expression of the Purkinje marker, calbindin (Fig. 1e).

Homozygous Cb Cln3Δex7/8 cells were first examined for JNCL-like characteristics. Homozygous Cln3Δex7/8 knock-in mice express multiple Cln3 mRNA splice variants and mutant battenin protein that is detectable by batp1 antibody recognizing C-terminal epitopes [12]. To assess this molecular phenotype in CbCln3Δex7/8 cells, RT-PCR and anti-battenin (batp1) immunostaining were performed. As shown in Figure 2, Cln3 mRNA isoforms in wild-type and homozygous cells were similar to those observed in total RNA isolated from wild-type or homozygous Cln3Δex7/8 knock-in brain, respectively (Fig. 2). In addition, batp1 immunostaining detected mutant battenin product in homozygous CbCln3Δex7/8 cells, in a similar albeit reduced cytoplasmic, vesicular staining pattern as that seen in wild-type cells. Batp1 signal exhibited some overlap with the lysosomal marker, Lamp1, but had more significant overlap with early endosome antigen 1 (EEA1) and the late endosomal marker, Rab7 (Fig. 3). Only limited overlap was observed with recycling endosomes, as determined by transferrin receptor co-staining (data not shown). Intriguingly, Lamp1 and EEA1 immunocytochemical distribution were altered in homozygous CbCln3Δex7/8 cells, with less perinuclear clustering than in wild-type cells, and Rab7 staining was frequently less intense in homozygous CbCln3Δex7/8 cells (Fig. 3). Heterozygous CbCln3Δex7/8 cells contained a mixture of Cln3 mRNA products from both the wild-type allele and the mutant allele, and batp1 signal was similar to that seen in wild-type cells (data not shown).

Figure 2

RT-PCR of Cln3 mRNA in wild-type and homozygous CbCln3Δex7/8cellsCln3 Exon1-forward, Exon 15-reverse RT-PCR products are shown, from total wild-type (+/+) or homozygous mutant (Δex7/8/Δex7/8) brain and cell line RNA. Brain and cell line RT-PCR reaction products had identical band patterns on ethidium-bromide stained agarose gels. Wild-type RT-PCR product was a single ~1.6 kb band and mutant products were ~1.6, ~1.5, ~1.4, ~1.35, and ~1.3 kb, representing multiple mutant splice variants.

Battenin and lysosomal and endosomal marker co-staining in wild-type and homozygous CbCln3Δex7/8cerebellar precursor cells Batp1 immunostaining of wild-type (CbCln3+/+) and homozygous mutant (CbCln3Δex7/8/Δex7/8) cerebellar precursor cells is shown, with co-staining for lysosomes (Lamp 1), early endosomes (EEA1), and late endosomes (Rab7). Significant overlap of Batp1 signal (red) with EEA1 (green, middle panels) and Rab7 (green, bottom panels) can be seen as yellow when the two channels are merged (Merge). The degree of Batp1 overlap is greatest with Rab7. Only limited overlap between Batp1 (red) and Lamp 1 (green, top panels) can be seen. Batp1 signal in homozygous CbCln3Δex7/8 cells is significantly reduced, but significant overlap with EEA1 and Rab7, and very little Lamp 1 overlap, can be seen as yellow in the respective merged panels. Notably, Lamp 1 and EEA1 localization appear altered, and Rab7 staining was frequently less intense in homozygous CbCln3Δex7/8 cells. Wild-type and homozygous CbCln3Δex7/8 confocal images were captured with identical exposure settings. 60 × magnification.

We next investigated the basis for subunit c accumulation, testing the hypothesis that cathepsin D is abnormal since it is required for ATP synthase subunit c degradation in the lysosome [13]. We first tested cathepsin D transport and processing in homozygous CbCln3Δex7/8 cells and Cln3Δex7/8 mice using anti-cathepsin D antibody that recognizes unprocessed and processed cathepsin D isoforms. Immunostaining of wild-type and homozygous CbCln3Δex7/8 cells revealed a perinuclear and punctate vesicular cathepsin D distribution, consistent with its transport and processing through the secretory pathway and delivery to the lysosome (Fig. 5a). However, in homozygous CbCln3Δex7/8 cells, cathepsin D distribution was less vesicular and more perinuclear-clustered than in wild-type cells. Immunoblots of homozygous CbCln3Δex7/8 cell and Cln3Δex7/8 tissue extracts also showed altered relative levels of cathepsin D isoforms (Fig. 5b). Cathepsin D isoforms, identified by relative molecular weights, represent the ~45 kDa precursor, the ~43 kDa intermediate single chain form of the enzyme, and the 31 kDa heavy chain of the double-chain form of the mature enzyme [14]. In homozygous CbCln3Δex7/8 cell and Cln3Δex7/8 tissue extracts, the precursor and heavy chains were reduced, and the single chain was slightly elevated compared to wild-type extracts. The cellular growth media did not contain altered levels of cathepsin D, indicating enzyme secretion was not affected. Heterozygous Cln3Δex7/8 mice and CbCln3Δex7/8 cells were indistinguishable from wild-type, as expected for a recessive disease phenotype (data not shown).

The impact of the altered cathepsin D processing on enzymatic activity was next tested to determine if altered enzymatic activity accounts for inefficient subunit c turnover. In a fluorogenic in vitro assay, cathepsin D activity in total cellular extracts was not significantly altered in homozygous CbCln3Δex7/8 cells (376 ± 89 RFU/μg total protein), versus wild-type cells (324 ± 58 RFU/μg total protein), although a consistent trend towards increased enzymatic activity in mutant cells was observed. Thus, cathepsin D transport and processing are disrupted in homozygous CbCln3Δex7/8 cells in a manner such that enzymatic activity appears to be relatively unaffected.

Homozygous CbCln3Δex7/8cells show abnormal membrane organelles

The abnormal transport and processing of cathepsin D suggested membrane trafficking disruptions in homozygous CbCln3Δex7/8 cells; therefore, we surveyed the subcellular distribution and morphology of membrane organelles. Components of the secretory pathway, including the ER, cis-Golgi, and trans-Golgi, did not appear altered from wild-type appearance when labeled with the respective markers, protein disulfide isomerase (PDI), GM130, and VVL (data not shown). By contrast, the lysosomal markers, Lysotracker and Lamp 2 had significantly altered signal in homozygous CbCln3Δex7/8 cells, versus wild-type cells. Wild-type cells exhibited brightly stained lysosomes that were large and clustered in the perinuclear region whereas homozygous CbCln3Δex7/8 lysosomes were lightly stained, smaller vesicles that were more diffusely scattered in the cytoplasm of the cell (Fig. 6). Lamp 1 distribution was also altered, as previously noted (Fig. 3). However, Lamp 1 and Lamp 2 total protein levels were similar in wild-type and homozygous CbCln3Δex7/8 cells by immunoblot analysis, indicating the altered signal likely reflects dispersed lysosomes or altered localization and/or epitope availability (data not shown). It is noteworthy that Lysotracker dye, which selectively accumulates in acidic compartments, exhibited the most marked reduction in lysosomal labeling. This observation may reflect altered lysosomal pH, an established finding in JNCL [10, 15].

Consistent with the altered early endosome marker (EEA1) signal observed by immunostaining (Fig. 3), fluid-phase endocytosis was also altered in homozygous CbCln3Δex7/8 cells, as measured by dextran-FITC uptake (Fig. 7). Following a 15-minute incubation in media containing dextran-FITC, wild-type and heterozygote cells displayed brightly stained, large endocytic vesicles that were clustered in the perinuclear region. However, homozygous CbCln3Δex7/8 cells were less brightly stained with most dextran-FITC signal localizing to smaller vesicles scattered throughout the cytoplasm of the cell.

Aging of homozygous CbCln3Δex7/8 cells at confluency is necessary to induce significantly accumulated subunit c protein. However, membrane organelle disruptions precede subunit c accumulation in homozygous CbCln3Δex7/8 cells, since they are observed without aging at confluency. Lysosomal and endosomal size and distribution are altered, and mitochondria are abnormally elongated and functionally compromised in sub-confluent homozygous CbCln3Δex7/8 cultures. These observations argue that membrane trafficking defects do not result from excessive subunit c accumulation compromising the lysosome, but rather are early events in the disease process preceding subunit c accumulation. Mitochondrial abnormalities, which have also been reported in JNCL patients and other animal models [21–23], may result from ineffective turnover by autophagy, a lysosomal-targeted pathway [24]. Alternatively, or simultaneously, battenin deficiency may impact mitochondrial function upstream of turnover, affecting mitochondrial biogenesis and/or altered transport and processing of mitochondrial proteins.

In wild-type CbCln3 neuronal precursor cells battenin primarily co-localizes with early and late endosomes. Battenin immunostaining in homozygous CbCln3Δex7/8 neuronal precursors is significantly reduced in abundance, but mutant signal also co-localizes with endosomal markers suggesting mutant battenin protein with C-terminal epitopes is trafficked similar to wild-type protein. In other studies, CLN3/battenin protein localization has been reported to partially overlap with late endosomes and lysosomes in non-neuronal cells [7], and to lysosomes, synaptosomes [8] and endosomes [9, 25] in neurons. These data jointly indicate that battenin resides in a subset of vesicular compartments linking multiple membrane trafficking pathways, perhaps functioning in vesicular transport and/or fusion. Endocytic and lysosomal-targeted pathways, including mitochondrial autophagy, are specifically implicated in this study.

Conclusions

The membrane trafficking and mitochondrial deficits uncovered in homozygous CbCln3Δex7/8 cells are likely to particularly impact neuronal function. Neurotransmission heavily relies on membrane vesicle transport, and a high-energy metabolism may further sensitize neurons to the loss of battenin activity. Thus, our panel of wild-type, heterozygous, and homozygous CbCln3Δex7/8 cerebellar cells provide an ideal model system to further elucidate battenin function and JNCL pathogenesis.

Genotyping and RT-PCR

Genomic DNA was extracted from tail biopsies and cell pellets as described (Cotman et al., 2002). Cln3Δex7/8 knock-in allele PCR genotyping was with wild-type primers, WtF (5'-CAGCATCTCCTCAGGGCTA-3') and WtR (5'-CCAACATAGAAAGTAGGGTGTGC-3') to yield a ~250 bp band and knock-in primers, 552F (5'-GAGCTTTGTTCTGGTTGCCTTC-3') and Ex9RA (5'-GCAGTCTCTGCCTCGTTTTCT-3') to yield a ~500 bp band. PCR cycling conditions were 95°C for 30 seconds, 58°C for 30 seconds, and 72°C for 35 seconds, repeated for 34 cycles. Total RNA isolation and Cln3 RT-PCR primers and procedures have been previously described [12].

Subunit c accumulation assay

Cells were seeded into 4-well chamber-slides (Falcon) at a density of 5 × 104 cells per well for microscopy studies, or into 100 mm dishes (Falcon) at a density of 5 × 105 cells per dish for protein extraction. Cells were typically >95% confluent one day post-plating, and the following day was considered 1-day post-confluency. At the indicated times, cells were either fixed with 4% formaldehyde in phosphate buffered saline (PBS), pH 7.4, for 20 minutes and processed for autofluorescence/subunit c immunostaining, or cell pellets were collected for total protein extraction.

Alternatively, cells were fixed with 2.5% glutaraldehyde/2% paraformaldehyde in 0.1 M cacodylate buffer, pH 7.4 for 1 hour and subsequently post-fixed and processed for TEM analysis as described [12]. In confocal microscopy studies, autofluorescent signal was observed over multiple wavelengths. For co-staining, settings were reduced such that autofluorescent signal did not contribute to antibody label signal.

Immunostaining and Immunoblot analysis

For immunostaining, cells were seeded at a density of 3–5 × 104 cells per well in 4-well chamber-slides and grown overnight at 33°C, unless indicated otherwise. Fixation was with ice-cold 4% formaldehyde in PBS, pH 7.4, for 20 minutes, or with ice-cold methanol/acetone (1:1) for 10 minutes at -20°C followed by air-drying (antibody-dependent). Cells were washed with PBS at least 2 times, 5 minutes per wash, between each of the following steps of the staining procedure: 0.1 M glycine in PBS for 5 minutes, 0.05% or 0.1% (antibody-dependent) Triton X-100 (Fisher Scientific) in PBS for 5 minutes, 2% bovine serum albumin (BSA) in PBS for 30 minutes, primary antibody diluted in 2% BSA/PBS for 90 minutes, secondary antibody diluted in 2% BSA/PBS for 60 minutes. All incubations were carried out at room temperature. Following staining procedures, slides were coverslipped with Vectashield mounting medium (Vector Laboratories) and analyzed on a BioRad Radiance 2100 confocal microscope (Biorad), with identical exposure settings for wild-type and mutant like images. All comparisons of wild-type and mutant staining were performed in Adobe Photoshop with identical brightness and contrast adjustments.

Cathepsin D activity assay

100 mm tissue culture dishes, which were approximately 80–90% confluent, were washed briefly with ice-cold PBS, and total protein extracts were isolated by scraping cells into 10 mM Tris, pH 7.4, 0.1% Triton X-100 followed by incubation on ice, for 20 minutes. The insoluble material was centrifuged at 14,000 g, the supernatant was isolated, and protein concentration was determined using the Bio-rad Dc Protein Assay. 50–70 μg of total protein extract were used to measure cathepsin D activity using the Fluorogenic Innozyme™ Cathepsin D Immunocapture Activity Assay Kit (EMD Biosciences) according to the manufacturer's recommendations. Relative fluorescence was measured using an Analyst AD plate reader (Molecular Devices) with the following filters and settings: excitation filter, 360-35; emission filter, 400-20, Flash lamp with 100 readings/well, 100 ms between readings, and 100,000 μs integration time.

Lysosomal staining and endocytic uptake

Cells were seeded at a density of 3–5 × 104 cells per well in 4-well chamber-slides and grown overnight at 33°C. Growth media was exchanged for fresh, pre-warmed growth media containing 500 nM Lysotracker or 1 mg/ml dextran-FITC, and cells were incubated at 33°C for 45 minutes or 15 minutes, respectively. Following labeling, cells were immediately placed on ice and washed for 10 minutes in ice-cold dye-free media, and fixed with 4% formaldehyde in PBS, for 20 minutes on ice. Chambers were removed and slides were coverslipped with Vectashield mounting media for confocal microscopy analysis, as described above.

Morphometric analysis of mitochondria

TEM photomicrographs (10,000 × – 40,000 × magnification) were taken from random grid fields. For length measurements, the longest side of each mitochondria was measured in centimeters, and along the length of the mitochondria, width measurements were taken every 2.5–4 mm (dependent on the magnification of the micrograph image). Following measurement, all numbers were normalized to reflect one magnification and data was analyzed using Microsoft Excel software. To ascertain unmagnified mitochondrial size, final measurement data, in centimeters, was converted to nanometers according to scale bar representation.

ATP measurement

ATP was measured by using the CellTiter-GLO® Luminescent Cell Viability kit (Promega), according to the manufacturer's recommendations. Briefly, cells were plated in a black opaque-walled 96 well plate (Packard Bioscience) at a density of 20000/well and incubated at 33°C overnight. The following day, CellTiter-GLO® Reagent was added to each well and cell lysis was induced by mixing 2 minutes. An ATP standard curve was prepared in the same plate. Before recording luminescence with a microplate luminometer (MicroLumat Plus LB 96V, Berthold Techonologies), the plate was dark adapted for 10 minutes at room temperature to stabilize the luminescence signal.

Hydrogen peroxide treatment assay

Cells were plated at a density of 10,000 cells/well in 96-well plates and incubated at 33°C overnight. The following day, fresh media containing varying concentrations of hydrogen peroxide was dispersed to each well. Cells were incubated in the presence of hydrogen peroxide for 24 hours, at 33°C, and viability was measured using the CellTiter-96® AQueous Non-Radioactive Cell Proliferation Assay (Promega), according to the manufacturer's specifications.

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Acknowledgements

The authors thank Dr. E. Kominami for antibody to subunit c of mitochondrial ATPase, L. Trakimas and M. Ericsson of the Harvard Medical School Electron Microscope Facility, Dr. David Sulzer for assistance with TEM analysis, Dr. Sylvie Breton for assistance with endocytosis experiments, and Dr. Andre Bernards and James Follen for assistance with the cathepsin D activity assay. This work was supported by NIH/NINDS grant # NS 33648. Dr. S.L. Cotman received fellowship funding from the Batten Disease Support and Research Association (BDSRA).

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Authors' contributions

EF participated in establishment and characterization of cell lines and performed ATP determinations. PW participated in mitochondrial analysis and immunocytochemistry. JE, TL-N, AMT, and HG participated in genotypic and additional phenotypic analysis of cell lines. DR and EC generated virus-conditioned medium for conditional immortalization of cells. MEM co-conceived of the study and assisted on drafting of the manuscript. SLC co-conceived of the study, participated in establishment and phenotypic analysis of cell lines, and drafted the manuscript. All authors read and approved the final manuscript.

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